CRISPR-Cas: Editing Life
The plan for all living things is written in the genes. The
central dogma of biology states that the flow of genetic information in a cell
goes from DNA to RNA to protein. The order of the four nucleotides that make
the business end of a DNA molecule codes for a gene and that sequential order
of the DNA code determines the protein to be made. The proteins, in turn,
provide a specific function to the cell and, subsequently, to the whole
organism. Life on this planet depends on the reliability of the information
stored in the DNA.
As we strive to learn more about the way life operates,
manipulating genes is a necessity for the molecular biologist. Cloning genes,
mutating genes, transferring genes are staples of the molecular biologist’s
toolbox that we use to manipulate and study genes.
New Molecular Tools
There have been huge strides in molecular technology since
the discovery of DNA as the chemical of inheritance in 1943 and the
determination of its structure in 1953, but manipulating genes for study is
still tedious, time-consuming, and expensive. There’s a new tool, though, that
is revolutionizing molecular biology like no other innovation since polymerase
chain reaction (PCR) in the late 1980’s. The new molecular tool is called,
Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR for short.
The start of the CRISPR path to glory began with the
discovery in 1987 of repeated spacer segments of DNA in bacteria that were
interrupted and clustered repeat segments instead of the typical consecutive
repeat segments. In 2002, it was discovered these unique repeat clusters were
associated with a common set of sequences coding for proteins that function to
modify DNA. This family of proteins was called the CRISPR-associated-systems,
or Cas.
Three years later, the CRISPR DNA sequences were found to be
similar to those of bacteriophage (viruses that infect bacteria) and plasmid
DNA (closed-circular pieces of extrachromosomal DNA that are passed between
bacteria). Several years later, the structure and functional pieces of the
CRISPR sequences and their associated Cas proteins puzzle fell into place and
the role of CRISPR-Cas was identified as an adaptive immune system for
bacteria.
DNA Search & Destroy
Foreign DNA from the bacteriophage or from a plasmid invader
enters the bacteria, gets chopped up, and unique pieces of DNA are remembered
as part of the CRISPR sequences in the bacteria’s genome. When the same or
similar foreign DNA threatens the bacteria a second time, the bacteria responds
with the search and destroy CRISPR-Cas complex. The CRISPR sequence binds to
its specific homologous sequence on the invader’s genome, the Cas protein cuts
the double-stranded invader DNA, and leaves the foreign DNA useless and to be
ultimately destroyed before it causing any damage to the host cell.
After identifying and streamlining the function of this
adaptive immune system of bacteria, several groups engineered the CRISPR-Cas9
system to be used as a gene editing tool in 2012. The CRISPR-Cas9 endonuclease
gene editing complex contains three basic components. The nucleic acid portion
containing the specific single-guide RNA (gRNA), an RNA bridge structural
portion, and the Cas9 endonuclease which binds to the bridge section.
Simple and effective.
The scientists discovered that, by designing and changing
the sequences of the guide RNA, one can target specific genes or sequences in
any genome, making a programmable targeting element to our search and destroy
system. The stage was set. Now, we had a powerful tool for gene editing.
Gene Editing in Research
For example, a researcher studying Gene X could now program
the system with guide sequences specific to Gene X, synthesize this specific
Gene X CRISPR-Cas9, and introduce it into the cell, where the complex will find
its homologous spot on Gene X and bind. The Cas9 endonuclease will cut the DNA
at a defined point of the genome.
When the cell tries to repair the break, insert or deletion
(indels) will occur forcing mistakes with the transcription and translation of
Gene X. The resulting Gene X protein is nonfunctional and its absence can be
studied.
Impact of CRISPR-like Gene Editing
I don’t know if there has been a molecular technology that
has affected the clinical/application side of medical science as rapidly as
CRISPR gene editing. The last great molecular revolution, PCR, was a game
changer in the research and development side of the field but took a decade
before it moved into the clinical side of the field. Even then, PCR was mainly
used as a screening/diagnostic tool.
CRISPR is different. Discovered in 2012, it was first used
in live animal studies within a year. That is a blink-of-an-eye in the normal
science time frame. In a few short years, the technology has exploded to
seemingly any molecular function imaginable. Plus, it is simple and cheap,
which is always a promising (but unique) factor in the development of new
technologies.
In his Huffington Post article, “Top 10 Tech TrendsTransforming Humanity”, Peter Diamandis, Co-founder/Vice-Chairman at Human
Longevity, Inc., includes a section titled “Glimpsing the End of Cancer &
Disease”. In this section, he lists ten 2016 technological advances in the
fight against disease and cancer. Four of the ten involve CRISPR-based gene
editing technology. From successfully treating an aggressive form of lung
cancer, to National Institute of Health (NIH) approval for a project to modify
the immune cells of 18 different cancer patients, to cutting HIV genes out of
live animals, to curing sickle cell disease by editing out the disease-causing
DNA sequences from mice, all are using CRISPR-Cas9 systems to advanced clinical
treatment.
That is pretty impressive for a three-year-old technology.
Gene Editing in Science Fiction
"Everything is possible with CRISPR. I'm not kidding." - Hugo Bellen, geneticist, Baylor College of Medicine
Mess with the DNA sequence, mess with the protein, mess with the organism. So what does all this gene editing stuff have to do with science fiction?
Potential.
Yes, potential. With gene editing and science fiction, it’s
like Dr. Bellen says, “Everything is possible…” As a writer who loves science fiction,
what is better than having a logical, powerful and incredible piece of actual
science that can open story doors and allow the manipulation of any living
thing?
If you want to get started, here’s a link to an excellent
short video about DNA basics from the Genetic Science Learning Center at the
University of Utah.
They also have a nice tutorial page about making proteins
from the DNA code with some cool stuff about the effect of mutations.
The Dark Side of CRISPR-Cas
As with most things, CRISPR gene editing is not perfect. It
has a dark side. Off-target effects. These off-target effects occur when the
CRISPR-Cas9 search and destroy complex binds to the genome at a secondary
target site where it is not supposed to bind. Although, there have been recent
advances in minimizing off-target effects, they still hinder the advancement of
this powerful technology.
But what is a bane for scientist can be a boon for the
science fiction author. Where off-site targeting can cause effects that ruin my
experiment, maybe these effects can result in a great twist for my sci-fi
novel. How about the formation of sentient strain of lab rats that form an
alliance to protect their lab animal care worker from funding cuts and layoffs?
Or a strain of edited soybeans that shows great protection from Fusarium root
rot but after a generation switches to rapid and uncontrollable growth that
overtakes the central plains?
There is great potential in the dark side of science.
See you all tomorrow.
Buh-bye.
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